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  • fastq-dump and paired end reads

    Already solved - sorry for the post.

    Hi,
    I downloaded all runs from a paired 50-nt reads experiment from SRA (SRP002274). When I use fastq-dump to generate fastq files (e.g. fastq-dump -A SRR039628 -D SRR039628.sra) everything works fine except that I only get a single file and not two pair files. It is not clear to me how I can identify read pairs from a single file since the read names only provide information about lane, tile, x and y but not "read pair number" (e.g. @SRR039628.1 HWI-EAS220_1_FC304WC_GEX:3:1:1056:45).
    I am probably missing something obvious so any help is much appreciated.
    Best,
    Moritz
    Last edited by moritz; 02-10-2011, 07:17 AM. Reason: Already solved - sorry for the post.

  • #2
    I think I found the corresponding read (same spot) in another file. Sorry for the post.

    Comment


    • #3
      dumping paired-end reads from .sra files

      Dear All,
      I am sharing an experience how to dump .sra file into fastq files. Always pass
      Code:
      --split-3
      flag to fastq-dump command. It will save forward and reverse reads in separate files. If the .sra file contains only the single end read only one fastq file will be generated.
      Thanks

      Comment


      • #4
        query

        kindly someone pls help me as to will the --split3 flag in fastq dump will surely generate a R1 and R2 file... as to I am not quite sure that my data is single ended or paired. when i converted using this flag and used for bowtie the result was as follows:
        102886046 reads; of these:
        102886046 (100.00%) were paired; of these:
        95447806 (92.77%) aligned concordantly 0 times
        3451944 (3.36%) aligned concordantly exactly 1 time
        3986296 (3.87%) aligned concordantly >1 times
        ----
        95447806 pairs aligned concordantly 0 times; of these:
        30023949 (31.46%) aligned discordantly 1 time
        ----
        65423857 pairs aligned 0 times concordantly or discordantly; of these:
        130847714 mates make up the pairs; of these:
        57243419 (43.75%) aligned 0 times
        46040125 (35.19%) aligned exactly 1 time
        27564170 (21.07%) aligned >1 times
        72.18% overall alignment rate



        I think this is not a good result for a paired seq.!!!


        kindly help.

        Comment

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